Skip to main content

Table 5 Overrepresented Gene Ontology (GO) categories of genes with transient body methylation

From: Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa

GO term Ontology description Number in input list Number in BG/Ref p-value FDR
Protein metabolism
GO: 0006886 P Intracellular protein transport 32 187 8.10E-13 1. 70E-10
GO: 0034613 P Cellular protein localization 33 199 8.90e-13 1. 90E-10
GO: 0030163 P protein cataolic process 19 156 6.50E 0.0011
GO: 00065111 P ubiquitin-dependent protein catabolic process modification-dependent protein catabolic 17 130 7.50E-06 0.0012
GO: 0019941 P process 17 130 7.50E-06 0.0012
Nucleic acid metabolism
  nucleobase, nucleoside and nucleotide
GO: 0055086 P metabloic process 28 256 4.80E-07 9.20E-05
GO: 0006259 P DNA metabolic process 25 214 5.60E-07 0.00011
Go: 0016070 P RNA metabloic process 87 1366 2.10E-06 0.00037
GO: 0034660 P nCRNA metablic process 24 141 5.90E-10 1.20E-07
GO: 0006396 P RNA processing 22 141 3.00E-06 0.00053
GO: 0006399 P tRNA metabloic process 20 108 3.30E-09 6.60E-07
Cellular signalling
regulation of small GTPase mediated signal
Go: 0051056 P transduction 13 63 4.80E-07 9.20E-05
GO: 0046578 P regulation of Ras protein signal transduction 13 63 4.80E-07 9.20E-05
GO: 0007265 P Ras protein signal transduction 13 63 4.80E-07 9.20E-05
GO: 0009966 P regulation of signal transduction 13 67 1.00E-07 0.00018
GO: 0023051 P regulation of signaling process 13 67 1.00E-06 0.00018
GO: 0010646 P regulation of cell communication 13 37 1.00E-06 0.00018
GO: 0032011 P ARF protein signal transduction 7 34 0.00022 0.029
  1. Genes were determined to be methylated at their gene bodies compared to a non-immunoprecipitated control using a negative binomial analysis (q < 0.1). GO analysis was performed with the AgriGo Singular Enrichment Analysis tool (http://bioinfo.cau.edu.cn/agriGO/analysis.php).Categories shown are a subset of the total 189 significantly enriched (p < 0.05) categories, all of which are shown in Additional file 3.